37. Pradinio High Scoring Segment Pair (HSP) praplėtimas Neighborhood Score Threshold Minimum Score Significance Decay
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Editor's Notes
Word above threshold deemed to be similar RDQ matched with REQ Next the BLAST algorithm now attempts to extend this alignment in both directions Cumulative score kept, results from tallying the matches, mismatches, and gaps Keeps going until optimal local alignment found
How does the algorithm know when an optimal local alignment has been found. Initial seed hit is extended All starts initially if the original “word” match is above the cutoff (T>11 – RDQ – REQ in our earlier example) The algorithm keeps a cumulative score (left axis) – addition for matches Once the mininum score S is reached a result will be returned – this result makes it to the BLAST output Algorithm keeps extending the alignment – addition for matches, negative for mismatches, gaps (dip in graph) Keeps extending alignment At some point, mismatches and gaps will outweigh matches and the cumulative score will drops off Another cutoff comes into play here to detect the lack of good alignment. (X) HSP trimmed back Resulting alignment is called the HSP – high scoring segment pair more than one HSP per sequence possible Show the length of the HSP on the graph
![Algoritmų taikymo sritis ,[object Object],[object Object],[object Object],[object Object]](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)